Loving the capital, and I'd love to get a look behind the curtain, I can think of a few neat things to do with that kind of module behavior.
I've been chipping away at the faction required material, slowly. I'm not sure what makes a faction hidden or minor but it would fit the flavour for sure. (The ships kind of clash when you see them too often.) As for missions - I never thought of that. But I'll put it on the list of things to work on since you're interested, thanks for the suggestion.
Hiding a hand-made market in a system file is pretty straightforward:
// Hide this market.
hiddenMarket.setEconGroup(hiddenMarket.getId());
hiddenMarket.setHidden(true);
hiddenMarket.setSurveyLevel(SurveyLevel.NONE);
primaryEntity.setSensorProfile(1f);
primaryEntity.setDiscoverable(true);
primaryEntity.getDetectedRangeMod().modifyFlat("gen", 5000f);
hiddenMarket.getMemoryWithoutUpdate().set(DecivTracker.NO_DECIV_KEY, true);
It's up to you how you'd want to place that market in the sector; anything from simply randomly assigning it to a procgen system via script to spawning an entire system with a semi-random location would work. Go nuts! I'm sure it'll be cool, whatever you come up with.
Missions are remarkably easy! One reason to have them is to serve as a sort of quickie showcase for people who want to try out your mod without starting a new campaign or opening up Console Commands.